If it were a very large company, I'd say you have a better chance with submitting on-line, because they will search all resumes for key words. If you submit it by hand, there is a great chance that it will be filed away. At a small company it won't matter as much. These companies may use headhunters to fill a lot of positions, on the mistaken belief that the headhunter will do the legwork in weeding out unqualified applicants.